Histone proteins are essential components of eukaryotic chromosomes, the objective of the study is to provide some new insights into its evolution through analysis of N. bombycis Histone genes at genomic level. In the study, genes encoding core Histone H2A, H2B, H3 and H4 from Nosema bombycis were analyzed by multiple sequence alignments. Analysis showed that: each type of the core Histone genes, sharing high similarity with each other in both coding and non-coding regions, has low copy number. Multiple sequence alignments showed N. bombycis core Histones diverge obviously, relative-rate test revealed Histone proteins have accelerated in the evolutionary rate of amino acid substitution. The distance between the stop codon and consensus poly (A) signal is compacted, no conserved hair-pin element was found in 3'-untranslated regions of Histone mRNAs and overlapping gene transcription was observed in the downstream region of Histone variant H3_3, that implies there maybe have only single class of core Histone genes encoding replication-independent Histones in N. bombycis. Surveying the upstream of the coding region of all core Histone genes, there were no canonical TATA or CAAT boxes except that a common Histone motif (TTTCCCTCC) was discovered. Moreover, no similar Histone motif mentioned above existed in Encephalitozoon cuniculi, the closely related organisms. That means that similar Histone motif maybe exists in microsporidian last common ancestor, N. bombycis retained Histone motif, while E. cuniculi have lost Histone motif after the differentiation from the common ancestor with the change of the host. Therefore the analysis of the genes encoding the Histones ofN. bombycis revealed that there maybe have two evolution directions in microsporidia, that is, genome extreme compact and mild compact, during the course of evolution. It contributes us to have the knowledge of that there have different genome size in microsporidia and provide useful information for understanding microsporidian biodiversity.